This explains the difference between validating the presence of a model vs an id.
With a model the object just has to be present to make the record valid. It does not have to be persisted yet. With the id, the validation ensures that the object is persisted before the assotiation is valid.
validates_presence_of :company_id and validates_presence_of :user
irb(main):001:0> user = User.new
=> #<User id: nil, name: nil, created_at: nil, updated_at: nil, company_id: nil>
irb(main):002:0> profile = Profile.new
=> #<Profile id: nil, user_id: nil, time_zone: nil, created_at: nil, updated_at: nil>
irb(main):003:0> company = Company.new
=> #<Company id: nil, name: nil, created_at: nil, updated_at: nil>
irb(main):004:0> profile.user = user
=> #<User id: nil, name: nil, created_at: nil, updated_at: nil, company_id: nil>
irb(main):005:0> user.company = company
=> #<Company id: nil, name: nil, created_at: nil, updated_at: nil>
irb(main):006:0> user.valid?
=> false
irb(main):007:0> profile.valid?
=> true
irb(main):008:0> company.save
(0.1ms) begin transaction
SQL (1.1ms) INSERT INTO "companies" ("created_at", "updated_at") VALUES (?, ?) [["created_at", "2015-10-07 13:23:40.041877"], ["updated_at", "2015-10-07 13:23:40.041877"]]
(0.6ms) commit transaction
=> true
irb(main):009:0> user.valid?
=> false
irb(main):010:0> user.company = company
=> #<Company id: 1, name: nil, created_at: "2015-10-07 13:23:40", updated_at: "2015-10-07 13:23:40">
irb(main):011:0> user.valid?
=> true
irb(main):012:0> user.save
(0.1ms) begin transaction
SQL (1.6ms) INSERT INTO "users" ("company_id", "created_at", "updated_at") VALUES (?, ?, ?) [["company_id", 1], ["created_at", "2015-10-07 13:27:30.753895"], ["updated_at", "2015-10-07 13:27:30.753895"]]
(0.6ms) commit transaction
=> true
irb(main):013:0> Company.destroy_all
Company Load (0.1ms) SELECT "companies".* FROM "companies"
(0.1ms) begin transaction
SQL (0.2ms) DELETE FROM "companies" WHERE "companies"."id" = ? [["id", 1]]
(1.3ms) commit transaction
(0.0ms) begin transaction
=> [#<Company id: 1, name: nil, created_at: "2015-10-07 13:23:40", updated_at: "2015-10-07 13:23:40">]
irb(main):014:0> user.valid?
=> true
irb(main):015:0> user = User.first
User Load (0.2ms) SELECT "users".* FROM "users" ORDER BY "users"."id" ASC LIMIT 1
=> #<User id: 1, name: nil, created_at: "2015-10-07 13:27:30", updated_at: "2015-10-07 13:27:30", company_id: 1>
irb(main):016:0> user.valid?
=> true
irb(main):017:0> user.company
Company Load (0.1ms) SELECT "companies".* FROM "companies" WHERE "companies"."id" = ? LIMIT 1 [["id", 1]]
=> nil
irb(main):018:0> User.destroy_all
User Load (0.1ms) SELECT "users".* FROM "users"
(0.0ms) begin transaction
SQL (0.3ms) DELETE FROM "users" WHERE "users"."id" = ? [["id", 1]]
(1.4ms) commit transaction
=> [#<User id: 1, name: nil, created_at: "2015-10-07 13:27:30", updated_at: "2015-10-07 13:27:30", company_id: 1>]
irb(main):019:0> profile.valid?
=> true
irb(main):020:0> profile = Profile.first
Profile Load (0.2ms) SELECT "profiles".* FROM "profiles" ORDER BY "profiles"."id" ASC LIMIT 1
=> #<Profile id: 1, user_id: nil, time_zone: nil, created_at: "2015-10-07 13:26:10", updated_at: "2015-10-07 13:26:10">
irb(main):021:0> profile.valid?
=> false